The 28-year-old Irishman will officially join the Dons when his current Tannadice deal expires.
Aberdeen boss Derek McInnes told the club's website: "I've always been a great admirer of Willo and he's a player I am looking to make a real impact for Aberdeen next season.
"With his extensive SPL experience, he was voted player of the year for Dundee United last season, which speaks volumes about his ability.
"We are delighted to have him on board as we look towards building a squad capable of bringing success back to the club."
Flood, who started his career at Manchester City, joined United on a free transfer from Middlesbrough in May 2011 after two previous loan spells at the club.
He has also played for Cardiff and Celtic as well as loan stints with Rochdale and Coventry as a youngster.